I just realized what made the game very memorable was the deep sense of conflict I could feel from my players when they made their decisions. It was not that they did something good or evil, it was because it was something so gray and difficult to accept that it provoked some interesting character responses.
I took me a while to find words to describe it, and I guess you can take my words with some skepticism because it is a GM tooting his horn. So I may be imagining it but when the PCs did what they did, I was also their audience and I was also pretty much in conflict of what happened.
Conflict and Doubt can be a strong source of emotional stimuli. Not having any right answers is pretty much what life is all about in my experience, but in real life we have no control so ordinary people are painted a darker tone - their weaknesses overwhelm their motives. While in a game or story, where you have real control, conflict does not have to end with frustration or a negative emotion.
The party did rescue most people, they did what was good for the Empire, even if it was not good for few people, and they didn't like having to hurt people and tried to avoid it. They had limits, there was scarcity, and they had other priorities that pulled them to many different directions. In that mess of forces there were many truths and many difficult decisions.
I'm not trying to reward any particular strategy, although forming a strategy and feeling and thinking through a problem I do admit strong bias towards. I guess I'm tooting my own horn. Although i do feel good about the conflict, and how I find what they did heroic and in how they handled the matter even with all their faults and weaknesses.
I may be suffering some confirmation bias, lolz. Still, when they felt conflicted Its only now I realize that is the strongest trigger of emotion I felt from the GM's seat. The conflict is the drama and what makes us love characters for their actions and their very human motives. This is probably my 21st gaming session I've GMed since coming out of retirement. Thats probably 52.5 hours of GMing (not counting preparing the games).
There is a finality in certainty, and in doubt and conflict the problem and the circumstance replays in many perspectives and many "Ifs".